No abstract

Genes of the major histocompatibility complex (MHC) have received much attention in immunology, genetics, and ecology because they are highly polymorphic and play important roles in parasite resistance and mate choice. Until recently, the MHC of passerine birds was not well-described. However, the genome sequencing of the zebra finch (Taeniopygia guttata) has partially redressed this gap in our knowledge of avian MHC genes. Here, we contribute further to the understanding of the zebra finch MHC organization by mapping SNPs within or close to known MHC genes in the zebra finch genome. MHC class I and IIB genes were both mapped to zebra finch chromosome 16, and there was no evidence that MHC class I genes are located on chromosome 22 (as suggested by the genome assembly). We confirm the location in the MHC region on chromosome 16 for several other genes (BRD2, FLOT1, TRIM7.2, GNB2L1, and CSNK2B). Two of these (CSNK2B and FLOT1) have not previously been mapped in any other bird species. In line with previous results, we also find that orthologs to the immune-related genes B-NK and CLEC2D, which are part of the MHC region in chicken, are situated on zebra finch chromosome Z and not among other MHC genes in the zebra finch.

In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of inbreeding and genetic load. We address this using whole genome sequence data of scimitar-horned oryx (Oryx dammah), an iconic antelope that has been subject to contrasting management strategies since it was declared extinct in the wild. We show that unmanaged populations are enriched for long runs of homozygosity (ROH) and have significantly higher inbreeding coefficients than managed populations. These patterns were associated with a partial deficit of highly deleterious mutations but a considerable excess of weakly deleterious mutations. These findings emphasise the risks associated with multiple generations of inbreeding and highlight the complex dynamics of mutation accumulation and purging in captivity. As wildlife management strategies continue to diversify, our study reinforces the importance of maintaining genome-wide variation in vulnerable populations and has direct implications for one of the largest reintroduction attempts in the world.

In most passerine birds, individuals attempt to maximize their fitness by providing parental care while also mating outside their pair bond. A sex-specific trade-off between these two behaviours is predicted to occur, as the fitness benefits of extra-pair mating differ between the sexes. We use nest observations and parentage analysis to reveal a negative association between male care and the incidence of extra-pair paternity across three species of penduline tit (Remizidae). This provides evidence of a trade-off between these two behaviours, possibly due to the devaluing of paternal care by extra-pair offspring.